The production chain of biofuels from agricultural residues in Mexico is analyzed, considering the maximization of the energy produced, the overall costs minimization and the mitigation of CO2 emissions. An analysis tool was developed through a comprehensive MILP model that takes into account all aspects of the supply chain with real data to define robust alternatives to widen the country's energy portfolio. The mathematical model considers different technologies for converting the residues generated throughout the country into three possible products. The results show that an adequate combination of fermentation and gasification technologies, and the selection of appropriate sites to locate processing plants and suitable consumers for the biofuels produced, would result on the net production of around 237 PJ per year of energy and enough ethanol to substitute all the Methyl Ter-Butyl Ether (MTBE) used in gasoline in Mexico, while preventing the emission of around 11 Tg of CO2 per year to the atmosphere. It is concluded that the use of agricultural residues as an energy source should be considered as a national policy in energy in which the state-owned oil company, PEMEX, can lead the project given its experience in logistics and nationwide presence, diversifying at the same time its portfolio of energy sources. (C) 2014 Elsevier Ltd. All rights reserved.